She looks pretty large to be drinking out of that. As they grow, they start needing deeper dishes. If they can't keep their faces clean, it might be causing problems.
But honestly, it's really hard to know what could be causing it, and treatment could just make it worse without a diagnosis. If it's fungal, then antibiotics will make it worse. If it's bacterial, then an anti-fungal ointment will make it worse. Is there any way you can get a vet or someone with waterfowl experience to look at her? If there is a waterfowl rescue group in your area, they might be willing to answer questions or look at pictures to help you come up with a diagnosis.
In any event, a little extra nutrition never goes amiss, so you might start by adding some baby vitamins to their water. Also, what are they eating? Is the food fresh this season (as opposed to a bag leftover from a previous season)? Where do they live--indoors in a brooder, outdoors in a pen, on straw, wood chips, etc.. ?